Add SBML template project

.github/workflows/test-force-example.yml

@@ -36,8 +36,8 @@ jobs:
         run: |
           cp -r . ${{ env.PROJECT_DIR }}
           cd ${{ env.PROJECT_DIR }}
-          # Yes to cell_based component and Python bindings, defaults otherwise, yes to confirm
-          printf '\ny\ny\n\n\ny\ny\n' | python3 setup_project.py
+          # Yes to cell_based component and Python bindings, no to SBML, defaults otherwise, yes to confirm
+          printf '\ny\n\n\n\ny\nn\ny\n' | python3 setup_project.py
 
       - name: Add MyForce to the project bindings
         run: |

.github/workflows/test-project.yml

@@ -36,8 +36,8 @@ jobs:
         run: |
           cp -r . ${{ env.PROJECT_DIR }}
           cd ${{ env.PROJECT_DIR }}
-          # Use prompt defaults, yes to final confirmation
-          printf '\n\n\n\n\nn\ny\n' | python3 setup_project.py
+          # Prompt defaults (no components, no Python bindings, no SBML), yes to confirm
+          printf '\n\n\n\n\nn\nn\ny\n' | python3 setup_project.py
 
       - name: Configure
         run: ${{ env.PROJECT_DIR }}/scripts/configure.sh

.github/workflows/test-python-project.yml

@@ -36,8 +36,8 @@ jobs:
         run: |
           cp -r . ${{ env.PROJECT_DIR }}
           cd ${{ env.PROJECT_DIR }}
-          # Yes to python bindings prompt and final confirmation prompt
-          printf '\n\n\n\n\ny\ny\n' | python3 setup_project.py
+          # Yes to Python bindings, no to SBML, yes to final confirmation
+          printf '\n\n\n\n\ny\nn\ny\n' | python3 setup_project.py
 
       - name: Configure
         run: |

.github/workflows/test-sbml-project.yml

@@ -0,0 +1,65 @@
+name: Test SBML Project
+
+on:
+  push:
+    branches: ["main"]
+  pull_request:
+    branches: ["**"]
+
+concurrency:
+  group: test-sbml-project-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test-sbml-project:
+    runs-on: ubuntu-latest
+
+    container:
+      image: chaste/base
+      options: --user root
+
+    env:
+      CHASTE_BUILD_DIR: /tmp/build
+      CHASTE_TEST_OUTPUT: /tmp/testoutput
+      PROJECT_DIR: /tmp/myproject
+
+    steps:
+      - name: Checkout template
+        uses: actions/checkout@v7
+
+      - name: Checkout Chaste source
+        run: |
+          git clone --depth 1 --branch develop https://github.com/Chaste/Chaste.git "${CHASTE_SOURCE_DIR}"
+          git config --global --add safe.directory "${CHASTE_SOURCE_DIR}"
+
+      - name: Install clang-format and curl
+        run: apt-get update && apt-get install -y clang-format curl
+
+      - name: Create test project
+        run: |
+          cp -r . ${{ env.PROJECT_DIR }}
+          cd ${{ env.PROJECT_DIR }}
+          # Prompt defaults for proceed/components/no-python-bindings, yes to SBML, yes to confirm
+          printf '\n\n\n\n\n\ny\ny\n' | python3 setup_project.py
+
+      - name: Install SBML code generator
+        run: ${{ env.PROJECT_DIR }}/scripts/sbml_install.sh
+
+      - name: Import the Goldbeter 1991 model
+        run: |
+          cd ${{ env.PROJECT_DIR }}
+          # Use the vendored model (examples/goldbeter_1991/Goldbeter1991.xml) so the
+          # job does not depend on reaching BioModels at run time.
+          cp examples/goldbeter_1991/Goldbeter1991.xml .
+          .virtualenv/bin/chaste_codegen_sbml Goldbeter1991.xml --model-type srn --output-dir src/
+          cp examples/goldbeter_1991/TestGoldbeter1991SbmlSrnModel.hpp test/
+          echo "TestGoldbeter1991SbmlSrnModel.hpp" >> test/ContinuousTestPack.txt
+
+      - name: Configure
+        run: ${{ env.PROJECT_DIR }}/scripts/configure.sh
+
+      - name: Compile
+        run: ${{ env.PROJECT_DIR }}/scripts/compile.sh
+
+      - name: Test
+        run: ${{ env.PROJECT_DIR }}/scripts/test.sh

README.md

@@ -8,6 +8,70 @@ Then see the [User Projects](https://chaste.github.io/docs/user-guides/user-proj
 
 If you clone this repository, you should make sure to rename the template_project folder with your project name and run the 'setup_project.py' script to avoid conflicts if you have multiple projects.
 
+## SBML models
+
+This template can turn an [SBML](https://sbml.org/) model into a Chaste model using
+[chaste-codegen-sbml](https://github.com/Chaste/chaste-codegen-sbml). For a complete,
+worked example see [examples/goldbeter_1991/README.md](examples/goldbeter_1991/README.md).
+
+### 1. Enable SBML support
+
+When you run `setup_project.py`, answer **yes** to:
+
+```
+Do you want to create an SBML user project?
+```
+
+### 2. Activate the virtualenv
+
+```sh
+source .virtualenv/bin/activate
+```
+
+(If you ever need to (re)install the generator by hand, run `scripts/sbml_install.sh`.)
+
+### 3. Convert an SBML model into a Chaste model
+
+```sh
+chaste_codegen_sbml my_model.xml --model-type srn --output-dir src/
+```
+
+* `--model-type` is one of `generic`, `srn` (sub-cellular reaction network), or
+  `cell-cycle`.
+* The generated class and file names are derived from the **input file name**, suffixed
+  with `Sbml`. For example `my_model.xml` produces `MyModelSbmlOdeSystem.{hpp,cpp}`, plus
+  `MyModelSbmlSrnModel.{hpp,cpp}` (for `srn`) or `MyModelSbmlCellCycleModel.{hpp,cpp}`
+  (for `cell-cycle`).
+
+### 4. Write a test
+
+Add a test under `test/` that `#include`s the generated model, then list it in
+`test/ContinuousTestPack.txt`. See the walkthrough for a full example.
+
+### 5. Build and run the test
+
+From the project directory (with `CHASTE_SOURCE_DIR` pointing at your Chaste source):
+
+```sh
+scripts/configure.sh   # register the project and configure the Chaste build
+scripts/compile.sh     # build the project
+scripts/test.sh        # run the project's tests
+```
+
+### The SBML base classes
+
+These live in `src/` and are required by the generated code:
+
+| File | Purpose |
+| --- | --- |
+| `AbstractSbmlOdeSystem.{hpp,cpp}` | Base ODE system for a generated SBML model. |
+| `AbstractSbmlSrnModel.{hpp,cpp}` | Base sub-cellular reaction network (SRN) model. |
+| `AbstractSbmlCellCycleModel.{hpp,cpp}` | Base cell-cycle model. |
+| `SbmlEventType.hpp` | Enum of SBML event types (e.g. cell division). |
+| `SbmlMath.{hpp,cpp}` | Math helper functions used by generated equations. |
+| `fortests/SbmlTestHelpers.{hpp,cpp}` | Utility helpers for tests. |
+| `fortests/SbmlTestOdeSolution.{hpp,cpp}` | `OdeSolution` recording per-step parameters, for tests. |
+
 ## Python bindings
 
 This template can build [PyChaste](https://chaste.github.io/) Python bindings for your